Background: The oriental river prawn (Macrobrachium nipponense) is an economically important aquaculture species in China. Methods: In this study, the genetic diversity and population structure of 12 populations were investigated using ten microsatellite markers. Among them, the Xiaolong Mountain (XLS) population is a cultured stock, while the Songjiachang Reservoir (SJC) population originates from the Yangtze River as an outgroup. Results: A total of 213 alleles were detected across 342 individuals, with an average of 21.3 alleles per locus. The observed heterozygosity (Ho) ranged from 0.362 to 0.902 (mean = 0.724), and the expected heterozygosity (He) ranged from 0.581 to 0.925 (mean = 0.805). Shannon’s diversity index (I) ranged from 1.224 to 2.810 (mean = 2.130). The polymorphism information content (PIC) varied from 0.532 to 0.920 (mean = 0.787), indicating high informativeness of the markers. Population structure analysis revealed a weak genetic subdivision with a subtle clustering signal (K = 2), but evaluation of LnP(K) indicated that K = 1 could not be confidently rejected. Pairwise Fst values ranged from 0.008 to 0.058, with high gene flow (Nm = 4.060–31.000), denoting low-to-moderate genetic differentiation. AMOVA showed that 98% of genetic variation resided within populations, with only 2% among populations (overall Fst = 0.020, p < 0.01). Nei’s genetic distances ranged from 0.094 to 0.277. Conclusions: Overall, the 12 populations of M. nipponense exhibited high genetic diversity, low-to-moderate genetic differentiation, and a weak population structure with most variation residing within populations. These findings provide valuable molecular markers for selective breeding and offer theoretical guidance for the conservation and sustainable utilization of M. nipponense germplasm resources, although the inferred population structure should be interpreted with caution given the weak differentiation signal.

Climate change has led to increasingly frequent and unpredictable droughts and high-temperature events, creating extreme conditions that profoundly impact the productivity of freshwater ecosystems. In this study, we evaluated the effects of extreme temperature and drought events on Nanwan Reservoir, a large, deep body of water in Xinyang, China, by assessing water quality and phytoplankton biomass. Field investigations were conducted during both high-temperature and drought (HTD) conditions in 2019 and normal-temperature and non-drought (NTND) conditions in 2020. HTD conditions significantly disrupted the thermocline and oxycline structures, leading to prolonged stratification during this period. Although phosphorus concentrations remained relatively stable across both periods, nitrogen levels were markedly lower during HTD events, indicating a possible shift in nutrient limitation from phosphorus to nitrogen. Additionally, a complex relationship between environmental variables and phytoplankton biomass was observed under HTD conditions. These findings advance our understanding of primary production responses to extreme weather events in Nanwan Reservoir, highlighting the importance of incorporating this knowledge into water resource management and ecological conservation strategies.